If you show a little more code, esp. how your perl script opens the output file, that may help. Your perl upgrade might be interacting with your current shell environment regarding "locale", What version were you using the last time it worked? What version did you upgrade to? In what OS?
Then, maybe a sample of the output you expect (e.g. as a snippet hex dump from a good file), along with a sample of what your upgraded perl is producing (also as a hex dump snippet).
Till then, there's nothing much we can do...
Update: BTW,the way to avoid unicode "interpretation" on output is to open the output file like this:
open( my $outfh, '>:raw', $filename ) or die "$filename: $!\n";
(but if the data you print to the output file handle has somehow been flagged as utf8 text, you might get a warning about that)
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